From: Cun Zhang (
Date: Mon Sep 27 2010 - 20:17:33 CDT

try to add pbc parameter when using trjconv, it may be mol or res,say

trjconv -pbc mol .....

For more information, run command 'trjconv -h', and the '-pbc' part in the

On Mon, Sep 27, 2010 at 5:58 PM, Joyce Tan <> wrote:

> Hi.
> I've extended my 5ns MD simulation for another 10ns using GROMACS. After
> the simulation completed, i've converted some of the trajectory frame into
> pdb format and the protein appear to break into parts as in the attached
> jpeg file. When I look back to the trajectory file, the protein is broken
> into parts, too with long lines connecting the parts. May I know why this
> occur and how to solve it?
> Thanks.
> Regards,
> Joyce